Then apparently any Voyager episode with Captain Braxton never happened, as he was from the 29th century.

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Braxton's people, as well as Daniels' 31st century time cops, are from the post-Endgame/Destiny future and always were. That's why they don't prevent Admiral Janeway from interfering in the timeline - their own existence depends upon it.

Then there's those ugly aliens from the 26th century trying to get their hands on the Tox Uthat in TNG: Captain's Holiday.

The problem though is it sounds like novels are being interpreted as canon here. What's to prevent an author from completely negating another author's work, if Paramount/CBS/Pocket/Whoever allows the brand name?

There's a(n infinite?) number of timelines that sprang forth from Janeway's victory over decency in Endgame.

Besides that 26th century was demolished/sidelined by Archer predestroying the sphere builders in the 22nd century who were no longer there to fight the Federation another 4 hundred years after their final routing.

Then there's those ugly aliens from the 26th century trying to get their hands on the Tox Uthat in TNG: Captain's Holiday.

The problem though is it sounds like novels are being interpreted as canon here. What's to prevent an author from completely negating another author's work, if Paramount/CBS/Pocket/Whoever allows the brand name?

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I didn't mean to give that impression. They're one possible way things could turn out though - at least as valid as any fan speculation.

I think I remember that in Vorloneese... Jingle, jangel jingle, jangle, jangle...

The truth points to itself.

Novels are cool, but not canon.

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Novels all written pre-Path to 2409 were all written pretty off the hip with the intent to try to make them mesh; however, anything after that point is pretty much considered heavy efforts to restart trekdom and hudge efforts were made to ensure continuity.

Besides, everytime that word canon comes up --- it is such a sloppy word. Canon quiet literally means what YOU accept as hardline continuity and thus makes it a very sloppy word to try to define something.

Trek lit tends to be used when canon gives insufficient information for a meaningful response.

As for the novels themselves - in the last decade, an effort was made to keep them in continuity.
The quality - generally good; lately, though, they gained a definite 'star wars lit' favour - every other book must be about a galactic catastrophe/war/etc.

I'm gradually forming a theory that each separate series, and each individual film, somehow take place in their own alternate universes from the TOS timeline. It might account for things that are almost the same, but slightly different from what's been established in previous efforts.

According to the novels, in every timeline except the one where the Destiny trilogy happened, the Borg assimilate the entire galaxy by the year 2600. Voth lose

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As per canon, that would be, at most 'in the majority of the timelines where the Destiny trilogy didn't happen, the Borg assimilate the entire galaxy by the year 2600':

Braxton tried to destroy voyager long before 'endgame', in 'future's end'. And he wasn't insane then; he would not try to do this if the entire galaxy (including earth) would be assimilated by his actions.

The first Braxton that tried to destroy Voyager did not have the technology to view/scan alternate timelines. He didn't even think that they existed. The other Braxton who turned up at the end did. These two different 29th centuries employed radically different temporal technologies, and one of them was blown up.

As per trek lit - Department of temporal investigations - federation temporal agents were informed as early as the 24th century that the timelines that don't include 'Destiny' end up with the entire galaxy assimilated; by the 29th century (and before), that was common knowledge*.
No temporal agent from Braxton's time would try destroying voyager before 'endgame' and condemning the entire galaxy - unless their timeline did not include 'destiny' and, as such, it was not a consideration.